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- PDB-5ewi: Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Direct... -

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Basic information

Entry
Database: PDB / ID: 5ewi
TitleCrystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90
Components
  • VRC38.01 Heavy Chain
  • VRC38.01 Light Chain
KeywordsIMMUNE SYSTEM / Fab / HIV-1 / V1V2 / Env / Antibody / Envelope / Neutralizing
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5996 Å
AuthorsGorman, J. / Kwong, P.D.
CitationJournal: Immunity / Year: 2017
Title: Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop.
Authors: Cale, E.M. / Gorman, J. / Radakovich, N.A. / Crooks, E.T. / Osawa, K. / Tong, T. / Li, J. / Nagarajan, R. / Ozorowski, G. / Ambrozak, D.R. / Asokan, M. / Bailer, R.T. / Bennici, A.K. / Chen, ...Authors: Cale, E.M. / Gorman, J. / Radakovich, N.A. / Crooks, E.T. / Osawa, K. / Tong, T. / Li, J. / Nagarajan, R. / Ozorowski, G. / Ambrozak, D.R. / Asokan, M. / Bailer, R.T. / Bennici, A.K. / Chen, X. / Doria-Rose, N.A. / Druz, A. / Feng, Y. / Joyce, M.G. / Louder, M.K. / O'Dell, S. / Oliver, C. / Pancera, M. / Connors, M. / Hope, T.J. / Kepler, T.B. / Wyatt, R.T. / Ward, A.B. / Georgiev, I.S. / Kwong, P.D. / Mascola, J.R. / Binley, J.M.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: VRC38.01 Heavy Chain
L: VRC38.01 Light Chain


Theoretical massNumber of molelcules
Total (without water)49,2752
Polymers49,2752
Non-polymers00
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-22 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.353, 84.775, 90.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-466-

HOH

21H-488-

HOH

31H-506-

HOH

41L-496-

HOH

51L-563-

HOH

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Components

#1: Antibody VRC38.01 Heavy Chain


Mass: 25151.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6N089
#2: Antibody VRC38.01 Light Chain


Mass: 24123.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01834
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 14% PEG400, 13% PEG8000, 0.1M Tris pH 8.5, 0.1M MgCl, No Cryo

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5996→50 Å / Num. obs: 63192 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.69 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Χ2: 0.96 / Net I/av σ(I): 16.759 / Net I/σ(I): 13.5 / Num. measured all: 403502
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5996-1.646.30.63641120.8450.2720.6930.71198.9
1.64-1.686.60.58441470.8930.2420.6330.74699.6
1.68-1.726.60.41841730.9280.1740.4530.79799.6
1.72-1.776.70.32241960.960.1340.3490.84999.4
1.77-1.836.70.24841810.9770.1030.2690.94699.7
1.83-1.96.20.31941850.9680.1390.3491.28399.7
1.9-1.976.20.27441860.9140.1210.31.25899.8
1.97-2.066.70.12242380.9910.050.1321.02199.8
2.06-2.176.70.09741790.9940.040.1051.04299.9
2.17-2.315.70.16142410.9590.0720.1760.91899.7
2.31-2.496.60.07542420.9960.0310.0811.03100
2.49-2.746.60.06442740.9960.0270.0690.95100
2.74-3.136.60.05942800.9970.0250.0640.936100
3.13-3.955.70.05442250.9960.0240.0590.99897.6
3.95-505.90.04843330.9960.0220.0530.93795.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XMK

4xmk


Resolution: 1.5996→31.176 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 2004 3.18 %
Rwork0.1731 61005 -
obs0.174 63009 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 28.2216 Å2 / Biso min: 4.73 Å2
Refinement stepCycle: final / Resolution: 1.5996→31.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 0 566 3902
Biso mean---35.5 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083459
X-RAY DIFFRACTIONf_angle_d0.9634713
X-RAY DIFFRACTIONf_chiral_restr0.057524
X-RAY DIFFRACTIONf_plane_restr0.006604
X-RAY DIFFRACTIONf_dihedral_angle_d11.1972078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5996-1.63960.2521330.20424238437197
1.6396-1.68390.26851500.191443134463100
1.6839-1.73350.20911290.18314332446199
1.7335-1.78940.22261550.180543164471100
1.7894-1.85340.20161350.178743464481100
1.8534-1.92760.32771400.25954318445899
1.9276-2.01530.2171490.19084319446899
2.0153-2.12150.21711400.17143644504100
2.1215-2.25440.24421470.19754360450799
2.2544-2.42840.24861420.18244359450199
2.4284-2.67260.20811460.166444164562100
2.6726-3.05910.18361430.165844354578100
3.0591-3.8530.1671450.15124428457398
3.853-31.18240.1631500.15544461461196
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.11070.35490.83462.40060.66132.03580.0335-0.1476-0.0855-0.00280.02110.05750.0122-0.1053-0.04480.0910.00170.00070.08450.01460.096229.8077-35.7824-14.6837
24.9301-1.35171.10461.5674-0.74432.2541-0.0252-0.13170.07630.07990.06410.1924-0.1147-0.5681-0.03860.19060.0274-0.01030.2343-0.03720.111815.9603-6.9354-8.8546
31.2126-1.05340.19142.9313-0.03241.5543-0.03170.07720.0113-0.0387-0.0113-0.0803-0.02780.00120.02320.097-0.01520.01260.0782-0.00420.082520.4972-31.0833-33.7475
42.34060.31490.85943.39390.77682.3013-0.09480.00050.40380.0039-0.0065-0.1955-0.28410.02150.06530.21150.0892-0.02040.1695-0.01820.209817.36253.891-20.928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 109 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 110 through 214 )H0
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 113 )L0
4X-RAY DIFFRACTION4chain 'L' and (resid 114 through 213 )L0

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